Permanent genetic memory with >1-byte capacity

Genetic memory enables the recording of information in the DNA of living cells. Memory can record a transient environmental signal or cell state that is then recalled at a later time. Permanent memory is implemented using irreversible recombinases that invert the orientation of a unit of DNA, corresponding to the [0,1] state of a bit. To expand the memory capacity, we have applied bioinformatics to identify 34 phage integrases (and their cognate attB and attP recognition sites), from which we build 11 memory switches that are perfectly orthogonal to each other and the FimE and HbiF bacterial invertases. Using these switches, a memory array is constructed in Escherichia coli that can record 1.375 bytes of information. It is demonstrated that the recombinases can be layered and used to permanently record the transient state of a transcriptional logic gate.United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4016)United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4018)United States. Office of Naval Research. Multidisciplinary University Research Initiative (N00014-13-1-0074)National Institutes of Health (U.S.) (GM095765)National Institute of General Medical Sciences (U.S.) (P50 GM098792)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SynBERC EEC0540879)FA9550-11-C-0028American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a